v1.5.13

• Minor fix: Correct logging / reporting of how many genomes were successfully downloaded using the new schema for downloading genomes from NCBI for a specific GTDB taxon.

What's Changed

• Raufs patch 1 by @raufs in #95

Full Changelog: v1.5.12...v1.5.13

v1.5.12

• Fix URL change related issues and add CARD as a database for lsaBGC-Pan minimal database creation via the -ld option in setup_annotation_dbs.py.
• Switch to a faster method for downloading bacterial genomes belonging to a common taxon in GTDB during prepTG database construction. Also, incorporate usage of the latest GTDB release R226.
• Edit: bump MIBiG version being used from 3.1 to 4.0.

Full Changelog: v1.5.11...v1.5.12

v1.5.11

• Major fix: If providing pre-made GenBank files for prepTG (e.g. from NCBI), there was previously a possibility where if some scaffolds featured entirely valid/expected CDS features, then partial GenBank files would be written and this would not simply result in skipping the genome as previously intended. Processing has now been substantially improved and options for prepTG around providing GenBank files to use as target genomes have changed.
  • Specifically, this issue would occur if a "translation" qualifier was missing for a CDS feature in some scaffold but present in every CDS feature of the first scaffold in a multi-record GenBank file.

Full Changelog: v1.5.10...v1.5.11

v1.5.10

• Add further requirement that the coordinate overlap between domain annotations when running zol in -dom mode be less than the minimal length allowed for domain-subunits (a user-adjustable parameter) as well as represent a maximum of 10% of the bps for the focal domain being considered.
• update remaining instances of query_name to query.name during HMM annotation partially addressed in the previous release.

What's Changed

• Update zol.py by @raufs in #94

Full Changelog: v1.5.9...v1.5.10

v1.5.9

Overview of Updates

• Incorporate BGC and viral scores into zol, cgcg, and cgc for ortholog groups based on Pfam annotations and mapping to weights from GECCO (by Carroll, Larralde, and Fleck et al. 2021 and scores from the V-Score database (by Zhou et al. 2024).
• Update code to account for TopHits.query_name being made redundant and removed in pyhmmer v0.11.0.
• Add safety checks to database downloading via setup_annotation_dbs.py

v1.5.8

Minor Updates

• When running in single-query mode in fai, fix construction of the final spreadsheet.
• Add shebang for script executables which were missing it.

What's Changed

• 1.5.8 by @raufs in #92

Full Changelog: v1.5.7...v1.5.8

v1.5.7

Minor updates

• Improve legibility/logic of code for domain coordinate determination - leads to difference in coordinates but not with consensus order/direction and gene-order inference on some test cases relative to the previous version.
• Add sorting to cases where for a functional database there are multiple tied best matching targets to the consensus sequence of an ortholog group to aid deterministic behavior for generation of zol consolidated reports.

Full Changelog: v1.5.6...v1.5.7

v1.5.6

• Corrected coordinates and consensus order/direction inference for zol "domain mode".

Minor improvements / fixes

• Make --select-fai-params-mode more robust to cases where input gene cluster instances only have 1 ortholog group in common and corrected outputing of FASTA output for near-core representative proteins (#88).
• Added flag in zol to avoid replacing start proteins with M if they are instead L or V based on direct translation if eukaryotic analysis is being performed: --eukaryotic-gene-cluster (#89)
• Correct generateSyntenicVisual.py usage with new setup which generates R scripts (#90).
• Updated cgcg to also work with results from "domain mode".
• Added options to control inflation parameter for MCL and to perform simple single-linkage clustering for ortholog group delineation (#91).
• Improved argument descriptions for prepTG, fai, zol
• Added overwrite / remove directory clearing for select fai/zol steps.
• Re-introduced edge weights in cgcg and added an option for minimum edge weight to show.
• Now report whether Beta-RD calculation is requested in the zol parameters file and also whether mge-annotation was used in prepTG
• Fixed salt being broken in update to v1.5.0
• Now right-strip "*" characters (stop codons) from sequences in prepTG databases
• Corrected automatic coloring in "instances" sheet of fai spreadsheet.

What's Changed

• update to v1.5.6 by @raufs in #87

Full Changelog: v1.5.5...v1.5.6

v1.5.5

Minor updates:

• Usually, environment variable OMP_NUM_THREADS is set to 1 on most systems, but, in case this is not the case, the environment variable is now set to 1 at the beginning of major executable programs.
• Add sorting when assigning locus tags to genomes in prepTG to make multiple runs more deterministic.

What's Changed

• Update CITATION.cff by @raufs in #85

Full Changelog: v1.5.4...v1.5.5

v1.5.4

• Fix possibility for zol to get stuck inside a while loop for determining the major/consensus path. Please avoid using v1.5.1 to v1.5.3!

Full Changelog: v1.5.3...v1.5.4